The ELIXIR Core Data Resources fundamental infrastructure for the life sciences, bioRxiv, 2019-04-05
AbstractMotivationLife science research in academia, industry, agriculture, and the health sector is critically dependent on free and open data resources. ELIXIR, the European Research Infrastructure for life sciences data, has undertaken the task of identifying the set of Core Data Resources within Europe that are of most fundamental importance to the life science community for the long-term preservation of biological data. Having defined the Core Data Resources, we explored characteristics of the usage, impact and sustainability of the set as a whole to assess the value and importance of these resources as an infrastructure, to understand sustainability to the infrastructure, and to demonstrate a model for assessing Core Data Resources worldwide.ResultsThe nineteen resources designated as Core Data Resources by ELIXIR together form a data infrastructure in Europe that is a subset of the wider worldwide open life sciences data infrastructure. These resources are of crucial importance to research throughout the world. We show that, from 2013 to 2017, data managed by the Core Data Resources tripled and usage doubled while staff numbers increased by only a sixth. Additionally, support for the Core Data Resources is precarious, with all resources together having assured funding for less than a third of current staff after only three years.Our findings demonstrate the importance of the ELIXIR Core Data Resources as repositories for research data and the knowledge generated from those data, while also demonstrating the precarious nature of the funding environment for this infrastructure. The ELIXIR Core Data Resources are part of a larger worldwide life sciences data resources ecosystem. Both within Europe and as part of the Global Biodata Coalition, ELIXIR will work for longer-term support for the worldwide life sciences data resource infrastructure and for the subset of that infrastructure that is the ELIXIR Core Data Resources.
biorxiv bioinformatics 0-100-users 2019Training and inferring neural network function with multi-agent reinforcement learning, bioRxiv, 2019-04-05
AbstractA central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose a new framework for optimising a recurrent network using multi-agent reinforcement learning (RL). In this framework, a reward function quantifies how desirable each state of the network is for performing a given function. Each neuron is treated as an ‘agent’, which optimises its responses so as to drive the network towards rewarded states. Three applications follow from this. First, one can use multi-agent RL algorithms to optimise a recurrent neural network to perform diverse functions (e.g. efficient sensory coding or motor control). Second, one could use inverse RL to infer the function of a recorded neural network from data. Third, the theory predicts how neural networks should adapt their dynamics to maintain the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death andor varying sensory stimulus statistics.
biorxiv neuroscience 0-100-users 2019Large-scale death of retinal astrocytes during normal development mediated by microglia, bioRxiv, 2019-04-04
Naturally-occurring cell death is a fundamental developmental mechanism for regulating cell numbers and sculpting developing organs. This is particularly true in the central nervous system, where large numbers of neurons and oligodendrocytes are eliminated via apoptosis during normal development. Given the profound impact of death upon these two major cell populations, it is surprising that developmental death of another major cell type – the astrocyte – has rarely been studied. It is presently unclear whether astrocytes are subject to significant amounts of developmental death, or how it occurs. Here we address these questions using mouse retinal astrocytes as our model system. We show that the total number of retinal astrocytes declines by over 3-fold during a death period spanning postnatal days 5-14. Surprisingly, these astrocytes do not die by apoptosis, the canonical mechanism underlying the vast majority of developmental cell death. Instead, we find that microglia kill and engulf astrocytes to mediate their developmental removal. Genetic ablation of microglia inhibits astrocyte death, leading to a larger astrocyte population size at the end of the death period. However, astrocyte death is not completely blocked in the absence of microglia, apparently due to the ability of astrocytes to engulf each other. Nevertheless, mice lacking microglia showed significant anatomical changes to the retinal astrocyte network, with functional consequences for the astrocyte-associated vasculature leading to retinal hemorrhage. These results establish a novel modality for naturally-occurring cell death, and demonstrate its importance for formation and integrity of the retinal gliovascular network.
biorxiv neuroscience 0-100-users 2019Suppression of unwanted CRISPRCas9 editing by co-administration of catalytically inactivating truncated guide RNAs, bioRxiv, 2019-04-04
AbstractCRISPRCas9 nucleases are powerful genome engineering tools, but unwanted cleavage at off-target and previously edited sites remains a major concern. Numerous strategies to reduce unwanted cleavage have been devised, but all are imperfect. Here, we report off-target sites can be shielded from the active Cas9•single guide RNA (sgRNA) complex through the co-administration of dead-RNAs (dRNAs), truncated guide RNAs that direct Cas9 binding but not cleavage. dRNAs can effectively suppress a wide-range of off-targets with minimal optimization while preserving on-target editing, and they can be multiplexed to suppress several off-targets simultaneously. dRNAs can be combined with high-specificity Cas9 variants, which often do not eliminate all unwanted editing. Moreover, dRNAs can prevent cleavage of homology-directed repair (HDR)-corrected sites, facilitating “scarless” editing by eliminating the need for blocking mutations. Thus, we enable precise genome editing by establishing a novel and flexible approach for suppressing unwanted editing of both off-targets and HDR-corrected sites.
biorxiv molecular-biology 0-100-users 2019The Genomics of Selfing in Maize (Zea mays ssp. mays) Catching Purging in the Act, bioRxiv, 2019-04-04
ABSTRACTIn plants, self-fertilization is both an important reproductive strategy and a valuable genetic tool. In theory, selfing increases homozygosity at a rate of 0.50 per generation. Increased homozygosity can uncover recessive deleterious variants and lead to inbreeding depression, unless it is countered by the loss of these variants by genetic purging. Here we investigated the dynamics of purging on genomic scale by testing three predictions. The first was that heterozygous, putatively deleterious SNPs were preferentially lost from the genome during continued selfing. The second was that the loss of deleterious SNPs varied as a function of recombination rate, because recombination increases the efficacy of selection by uncoupling linked variants. Finally, we predicted that genome size (GS) decreases during selfing, due to the purging of deleterious transposable element (TE) insertions. We tested these three predictions by following GS and SNP variants in a series of selfed maize (Zea mays ssp. mays) lines over six generations. In these lines, putatively deleterious alleles were purged, and purging was more pronounced in highly recombining regions. Homozygosity increased more slowly than expected; instead of increasing by 50% each generation, it increased by 35% to 40%. Finally, three lines showed dramatic decreases in GS, losing an average of 398 Mb from their genomes over the short timeframe of our experiment. TEs were the principal component of loss, and GS loss was more likely for lineages that began with more TE and more chromosomal knob repeats. Overall, this study documented remarkable GS loss – as much DNA as three Arabidopsis thaliana genomes, on average - in only a few generations of selfing.
biorxiv genomics 0-100-users 2019Allododecaploid yeasts synthetic hybrids of six species, bioRxiv, 2019-04-03
AbstractPolyploidy generates diversity by increasing the number of copies of each chromosome. Many plants, animals, fungi, and other eukaryotes are ancient or recent polyploids, including some of the best-known evolutionary radiations, crops, and industrial organisms. Polyploidy facilitates differentiation and adaptation to new environments, but the tools to test its limits are lacking. Here we develop an iterative Hybrid Production (iHyPr) method to produce allododecaploid yeast strains with a base ploidy of 12n. Chromosomal instability increased dramatically as additional copies of the genome were added. These six-species hybrids rapidly improved their fitness during adaptive laboratory evolution. This new method for making synthetic hybrids will enable basic research on polyploidy, cancer, and chromosome biology, as well as more applied research on biofuels, bioproducts, and synthetic biology.One sentence summaryWe constructed six-species synthetic hybrids and showed that they were chromosomally unstable but able to adapt rapidly.
biorxiv genetics 0-100-users 2019